I had a quick peek at Chris Mooney's paper, "Do scientist understand the public?" Worryingly, examples where he holds out where the relationship between the two seem to be working out reasonably were all cases were engagement occurred right at the start when the scientific information was just starting to trickle out.

In at least one of those cases (vaccination), there may have been no way for scientists to get out an engage in advance. Indeed, science had won. Vaccination was accepted as routine for decades. Then, panic emerged in the 1990s or so in various forms. And again, there's little discussion of how to deal with such flare-ups: "crisis communication" gets about half a paragraph.

Maybe those are good models. But it's still incredibly frustrating that they provide no insight on how to resolve issues where the science is as clear as it ever gets, and large numbers of nonscientists simply discount it. You know the issues: evolution, vaccination, climate change, etc. On subjects like these, Mooney all but throws in the towel:

Battle lines have hardened... and it may be far too late to “fix” the situation.

The word "fix" didn't need scare quotes in that sentence. The disconnect is a problem, and it does need to be fixed.

Additional: I rather like some of the commentary made by Evil Monkey here.

29 June 2010

Tropical storm. probably soon to be Hurricane, Alex is heading our way. The previous hurricanes that have had this sort of trajectory haven’t really done much more than a thunderstorm, so I’m not terribly worried. The university, though, decided to close. The initial announcement was for three days, although that was earlier in the day when the project ed path was straight on top of us.

We’ll see. Minimally, I’ll be playing Wii games working at home for tomorrow at least.

28 June 2010

Several people disagreed with my previous post about academic reprisals. So it seemed to me worth trying to explore the problem further.

It seems to me scientists fear reprisals because there are two things that they want:

Publication in high visibility journals, the “glamour mags.”

Grants.

Those two resources have two features that make the threat of reprisal genuine:

Anonymous peer review.

Scarcity.

Dealing with fear of reprisals at the level of the scientific community is a multi-part problem, each with different solutions.

The publishing model for journals is changing under our feet right now, and I think many of those changes are going to be good for breaking the prospect of reprisal. There are more and more venues where someone can publish, and it’s unreasonably to think a rival can block them all.

Journals are also promising targets for change because each one is independent. One dedicated editor or publisher can change how that venue works. There may be some limits to that, as Medical Hypotheses showed, but overall, editorial boards could really be change agents on this issue if they want to be.

Grants... much harder. This may be a situation where (gasp!) the politicians force change in federal funding. Transparency and accountability are fairly big issues for governments. Listen to this story (Part 2) about the G8/G20 and listen for how often “transparency” and “accountability” are mentioned.

Obviously, I advocate far more transparency in the review process. Just this morning, the editor-in-chief pf the British Medical Journal argued that the lack of accountability in peer review was a problem. This is the overwhelming direction the rest of the world is taking, governments and business and non-governmental organizations alike.

To that end, I’m giving up reviewing anonymously. And I’ve already started. I submitted some reviews over the weekend, and I signed them. I don’t know if the person in charge will keep my name on them, but there’s not a lot I can do about that.

I realize that I’m in an unusual situation that makes it easier for me to try to put my money where my mouth is. I don’t need six figure grants to do my research. I’m probably never going to have a paper in one of the fancy journals. I’ve sort of self-selected myself out of the rat race.

25 June 2010

A while ago, I wrote about a paper that argued that genes that define boundaries in the nervous system seemed to be responsible for differing brain structures in cichlid fish. This seemed to explain the data better than a competing hypothesis, which was that the differences in brain size were caused by the length of time the brain spent forming neurons (neurogenesis). A forthcoming paper by Charvet and Striedter suggest a third possibility.

Bobwhite quails (pictured) have kind of small brains. But that’s okay, because they’re kind of small birds; they’re smaller than a chicken.

But despite the chicken having a bigger brain, the chicken goes from fertilization to hatching faster than the bobwhite quail.

Proportionately, both the quail and chicken start neurogenesis at about the same time. The chicken has a slight edge, but the extra 5% of time the chicken spends doing neurogenesis isn’t enough to explain that the chicken’s brain ends up being 100% bigger than the quail’s. When neurogenesis starts, the chicken’s brain is already 100-200% bigger than the quail’.

Before neurons form, the chicken’s cells are diving great guns. The whole cell cycle, everything mitosis related, is ramped up and going at a much faster clip in chicken than quail. They tested this using bromodeoxyuridine (BrdU), a chemical that cells incorporate into themselves if they’re actively dividing. The more a cell divides, the more BrdU it takes in. They couldn’t test all the way through development, but at around 11% development, chicken are showing cell division going about 100% faster than quail. After neurogenesis begins, though, that difference is almost nil.

To sum up: The chicken makes a mess of cells real fast, real early.

The other two mechanisms are more about changing the relative proportions of regions within a brain: enlarging over here, shrinking over there. This mechanism allows you to make brains that are different sizes, but that are otherwise structurally similar.

The unanswered question, though, is why do chickens need such large brains?

Sometimes, the scientific literature sucks at getting information to you.

I was looking at the table of contents of a new issue of The Journal of Crustacean Biology and saw an article about how to photograph soft-bodied crustaceans. Hm, I wonder why photographing soft-bodied crustaceans is difficult, I thought.

And the abstract mentioned software to deal with short focal planes by merging several pictures. The software is Helicon Focus.

Yes, I should be happy that I have found something useful, but... dagnabbit, why didn’t I know about this years ago?

For instance, here’s part of Figure 3 from a paper a few years back (Espinoza et al. 2006) on the left, compared to a new picture processed with Helicon Focus (click to enlarge).

These are neurons stained through a technique called backfilling. The best backfills are really superb, and you can see a lot of detail. But they’re often in thick tissue, and neurons go all over the place through it, making it hard to see all the relevant detail. The way people usually got around this was to get a camera lucida attached to a drawing tube through a microscope, then trace the axons as you focused up and down.

I was actually very pleased with the pictures in Figure 3 as published, which had dark cells against a very clear background. But the one shown here on the left shows the problem of getting all the relevant detail in the shot. The cell bodies on the right are okay, but the ones down a little deeper in the ganglion on the left and their axons are already blurring out.

The processed version on the right is better.

Having played with this a bit, sometimes there are things you can see in the individual frames that do get lost in the processed version. The biggest problem is when there is some detail underneath something else. You can often see it under the scope and in the individual frames, but not so well in the composite image.

This was so startling and so useful to me, I briefly entertained the thought of trying to turn this into a neuroscience methods paper. Then I looked and found short references that it had been used in the invertebrate neurobiology literature a couple of years ago (Scanell et al. 2008) in a journal I read. D’oh! Another shrewd Faulkes scheme bites the dust.

But at least I can spread the word through a blog post. A slightly more recent paper by Berejnov and company (2009) has nothing whatsoever to do with biology, but gives a better example of what you might get from this kind of software.

As I was writing this, I read an interview with Neil Gaiman, where he said this, mostly in relation to book publishing in particular genres:

Information used to be gold: hard to find, expensive, the equivalent of going off into the desert and coming back with a perfect lump of gold. Now, it’s the equivalent of going off into the jungle, in which there is information everywhere and what you are trying to find is the piece that is useful, while ignoring the noise.

I do wish the process of finding useful things was a little less jungle-like.

23 June 2010

One of the things that bugs me it is that commenting is anonymous. My position: Anonymity doesn’t improve things (see here and here). The ostensible reason it is the way it is because people “fear reprisals.”

Has science become that much like the mob?

Are we as a group that thin-skinned, petty and vindictive that we’re going to put out a hit someone’s grant or whack another scientist’s pub because they didn’t think we used the right statistical test?

Besides, anyone who believes they can safely remain anonymous on the web is fooling themselves. Own every word you speak.

Personally, I doubt I’ll be commenting on papers on The Third Reviewer website, for much the same reason John Stewart doesn’t use Twitter: He has a TV show. I have a blog. If I have something substantive to say, I’ll say it here.

I wish the guys behind the site luck, because I think they’ll need it. The history of researchers commenting on published papers is... not encouraging. Many papers on, say, PLoS ONE don’t even a star rating, which is also anonymous, but much easier than writing a specific comment.

I read some time ago that phone text messages were the most common means of communication in the world, by a wide margin, surpassing email. It’s increasingly obvious to me in the way I use my own computer. I have my RSS reader and Twitter running all the time in addition to my email.

I want to be able to type a text message, click the mouse button, and have it sent to all the students in the class who want to receive texts.

I hacked a crummy solution in the spring semester: I created a list of students in Google Voice. The problem was, I could only send one message to one person at a time. So I had to cut and paste and send for each student. The list was short, so it didn’t take up that much time, but it took minutes when it could have taken seconds.

If anyone has a solution... yeah, I’m a dinosaur, email me.

Photo by neutralSurface on Flickr, user under a Creative Commons license.

22 June 2010

For a long time, people sort of overlooked those two factors. The teeth were obvious, but the venom wasn’t. Instead, people suggested that one of the ways that the slow moving monitor lizards were able to take down large prey was because their mouths contained so many bacteria, that the bitten prey animal got infected, quite quickly, and went down from the bacteria.

The discovery of venom seemed to put the kibosh on that particular story – the prey die too fast for bacteria to be the cause of death. But it doesn’t change the fact that the mouths of Komodo dragons are loaded up with very nasty bacteria.

Bull and colleagues take a totally different approach to this question. Rather than asking what the bacteria do for the Komodo dragons, they ask what the Komodo dragons do for the bacteria.

They hypothesize that the way to view the relationship is using a disease model. Bacteria are spreading from dragon to dragon in an epidemic fashion. The bacteria spread from dragon to dragon by growing on the large kills that dragons make, which are often fed on by several different individuals. The dragons’ prey almost becomes an intermediate host; a means of spreading from dragon to dragon.

They are not suggesting that the bacteria are harming the Komodo dragons or causing them to become sick, which seems a bit of a strange bending of the word “disease,” but at least they warn us.

It’s an interesting way of looking at the problem. There’s no experimental evidence presented here that it allows you to make better predictions about the bacteria or the dragons, though.

The National Center for Science Education is reporting that the Institute for Creation Research’s (ICR) lawsuit has suffered a powerful defeat.

But being rules that they brought no actual evidence was not enough. (Hey, since when has a lack of evidence ever bothered a creationist?) If you read previous entries in this series, you may recall that documents submitted by ICR as part of the lawsuit were described by external observers as “gloriously insane” and “20 pages of non-stop, thigh-slapping hilarity.”

I am sorry, but I have little sympathy for the ICR, and enjoy this part of the judgement against them.

It reads best if you imagine a dramatic pause where each comma sits in the sentence:

Plaintiff is entirely unable to file a complaint which is not overly verbose, disjointed, incoherent, maundering, and full of irrelevant information.

BOOM!

That’s got to sting. Just a little. Even for people with notoriously thick hides.

A close up of the very last appendages of a stomatopod, the uropods of Hemisquilla californiensis. Stompatopods can probably appreciate more of this colour than we can, having the most complex eyes in the animal kingdom.

Photo by Michael Bok on Flickr, used under a Creative Commons license. Michael also blogs at Arthropoda; check it out!

21 June 2010

You might expect a paper whose title starts with “Neural control” to include neurons.

This new paper by Liden and collegues doesn’t. It’s straight behaviour paper in the style of classic neuroethology. It starts by explicitly trying to tie itself to a hot new field: neuroeconomics. Neuroeconomics is about value assessment and decision making in humans. In many cases, this means doing brains scans of people while they play with experimenter’s money.

Liden and company argue that humans are far too complicated (which is true), and the way to go about understanding how you make decisions is by looking at an escape system. Escape systems are reasonably simple in terms of neurons, and they definitely control a decision: Fight or flight? Or, in the case of crayfish, freeze or tailflip?

When crayfish see a large dark object looming over them, they can freeze, or perform an escape tailflip. The experimenters put crayfish in a tank, and passed shadows over them. They did record from the giant pair of escape neurons that trigger visual escape responses, but they way they used those recordings was as a marker for whether an escape tailflip occurred.

Not surprisingly, when you change the stimulus the crayfish gets, the behaviour changes. Speed the shadow up, and the crayfish is more likely to freeze. But if the crayfish does tailflip, it “decides” to do so in less time.

The big finding that has the authors tooting the neuroeconomics horn is that if you put a strong smell of food in the water, the animal is more likely to freeze than if there’s very little smell of food. This, the researchers argue, means that the crayfish moderating the use of its escape behaviour due to the presence of the food, because the escape would be costly in that it would take the animal away from the food it wants.

But. This effect happens only at one of two shadow speeds that they tested. The effect does not appear to be very robust.

There are just two two problems with integrating this sort of study into the fold of neuroeconomics:

The neurons.

The economics.

As for the neurons, the title of this paper implies that it’s found how these neurons make decisions, but this paper only suggests what to look for. It doesn’t give new discoveries at the neuronal level. There are no new neurons or synapses or neurotransmitters described here.

And the search isn’t going to be easy. The main neurons that make the escape decision in these cases are medial giant (MG) neurons. While the MG axons are well known (they run throughout the crayfish’s body), the bit where all the interesting integration is going on – the place where sensory neurons and interneurons are connecting with the MGs – are nearly a complete mystery, tucked away inside the crayfish’s brain. A while ago, I went looking in the scientific literature for any good picture or diagram of the MG cell bodies and dendrites in the brain – and came up empty handed.

I’m glad that the authors are working with the MG-mediated escape responses; they’re overdue for attention. But make no mistake, the low level of information about them is a bug, not a feature, for crayfish escape as a neuroeconomics model.

As for the economics, it seems difficult to assign values in this situation. Human economics is pretty easy: $20 is better than $10, but not as good as $50. Having a standardized interval scale makes some of the most interesting neuroeconomics research possible.

But what is the value of the smell of food? What is the cost of tailflipping? An escape tailflip is very brief, and it doesn’t take the animal very far from the food. The authors point out that crayfish who win fights gain access to food – which is true – to argue how important food resources are to crayfish. What they don’t mention is that will crayfish fight in the complete absence of food or any other resource. The advantages that crayfish gain through fighting are subtle enough that it took several decades of research before people figured out that there were any resource advantages gained by winning fights.

It’s also worth noting that these experiments are very similar to some theoretical models about the regulation of crayfish behaviour. Don Edwards (a former supervisor of senior author Jens Herberholz) wrote a paper discussing how a crayfish might choose between different behaviours (getting food, escaping a predator) back in 1991. The results of that computer model feel very much like the results presented here.

Indeed, thinking back to the 1990s, there were a lot of important papers on how crayfish escape responses were modulated via changes to the lateral giant (LG) interneuron circuit (e.g., Yeh et al. 1996). The changes were caused by social interactions, so this was pitched as a model for... human aggression!

All these little moments of “spin” in this paper seem to have carried through to how the paper has been promoted. This press release, from the interesting (albeit sometimes dodgy) Science Direct is a testament to good marketing. There’s another press release here. Here’s a snippet from one:

(A) new line of research that may help unravel the cellular brain activity involved in human decisions.

Yeah, and if I don’t clean out my fridge, I may help develop a new antibiotic.

This is good research. But to say that it’s going to help us understand human decision making? Not yet. Not by a long shot.

P.S. – I have to bust the authors and reviewers’ and editor’s chops for letting this get into the paper:

(D)ifferences were not statistically significant although only marginally(.)

A p value is either significant, or it is not. It is not legitimate to treat the p value as some sort of direct indication of the “reality” or the size of an effect; see Schmidt (2010) for more.

Shameless self-promotion! For those who might want more information on the crayfish escape system, I wrote a review on this, focusing on the evolution and diversity of the behaviour and the underlying neurons responsible for it (Faulkes 2008).

19 June 2010

This picture was not taken in an aquarium filled with water; it’s in air.

The fish is a blenny, Alticus arnoldorum, and a new paper introduced me to this fish that barely deserves to be called a fish. According to the author, Shi-Tong Hsieh, this fish spends so much time on land that it actively defends territory on land. It can stay out of water indefinitely, as long as it stays moist.

That blows my mind.

Hsieh was interested how blennies were able to be so agile on land, so she recorded high speed video of several species and did detailed analysis of the movement. The leaping blenny above is the most active on land.

The big finding is that these terrestrial blennies are able to rotate their tail. That it, they can move it clockwise or counterclockwise relative to the axis of their bodies, not simply move it back and forth. When these fish jump, they are pushing off with the side of their tails, not the bottom.

The terrestrial blennies are able to jump about twice as far as their aquatic relatives, which can’t twist the tail. Although there isn’t enough evidence to say that this ability to rotate the tail caused the performance increase, it certainly is mighty suspicious.

Hsieh suggests that this jumping behaviour may be related to C-starts, which are fish escape responses I’ve mentioned before here and here. This would be tricky to test: the neurons are huge, but active behaviours like jumping make it difficult to record the activity.

An easier follow-up would probably be to start looking closely at the musculature and innervation of these terrestrial blennies to figure out exactly what has changed in the skeleton and / or muscles that allow them to do the twist.

18 June 2010

This seems to me like a coded argument to thin the competition for resources by deciding, a priori, that certain kinds of research are “a problem.” It’s balkanization (see also here).

By their argument, whole swathes of scientific endeavor should just... go away. Do we really want nothing but cancer research? Because that’s the kind of thing that would happen under their scheme. Biology would become medical research and not much else.

Arguing that certain kinds of research aren’t worth doing is arguing for ignorance. Sorry, but as far as I am concerned, knowledge is better than ignorance.

ARGH! (If you were in my office, you’d be hearing the greatest hits of “What is your favourite curse word?” from the Pivot questionnaire.)

Now, please excuse me. I have to go back to destroying science by writing my latest manuscript.

Although I’ve been blogging a long time, it’s only in the last couple of years that I’ve started to get serious about it, and social media (as these various channels have become known). I have developed a little online network of people I like to follow, and who, I would like to think, find at least some of what I have to say useful.

Yet as I’ve grown this online network, I’ve become more and more aware of the physical isolation of where I live. As I like to put it, “South until there ain’t more south to go.”

Twitter has probably been the biggest contributor to this increased awareness of isolation. Because Twitter is conversational, it is surprisingly spatial. People talk about where they are going to, who they are going to meet, and so on. Watch long enough, and you start to see some of the people you know crossing paths with each other.

Watching that traffic of information on the net emphasizes the long time I would have to to spend in traffic on the roads to have the face to face interactions others talk about. And I’ve noticed people in other parts of the country sometimes don’t understand the distances involved. “No, you don’t get it. I would have to get up early and drive all day to do that.”

Sure, now I can blog, tweet, and do other sorts of things from where I am and try to create involvement with my research colleagues in ways that I never could have before.

But damn it, there’s still nothing like face to face interaction. Face to face is about the joy of spontaneity, whereas online is about the admiration of the composed.

17 June 2010

Academia is supposed to be a meritocracy: You rise through the ranks because your work (and, by extension, you) is better than someone else’s. I think this emphasis on merit might be doing people a disservice, in a couple of ways.

The entire process de-emphasizes happenstance and luck. People chase and chase and chase after those grants and high impact publications, figuring that if they just work that much harder, they must get them. Particularly in tight financial times like these, where there are more proposals and papers submitted than can be published, you’re essentially playing a lottery. There is just no way to be that much more outstanding than all the other bright people to ensure success.

And I think this can be very demoralizing for people. Academics are usually very bright people. For much of their lives, things have often been relatively easy for them academically. They do well in school, through their undergrad degree, grad school, and so on.

But then they start reaching the point where things aren’t working as well as one would hope. They get a job at an undergrad university instead of that major research university you’ve been working towards for a decade or more. They don’t get the grant. Again. You can’t get the publications in the journals you want. And when these things happen? There’s that little niggling voice in the back of your head saying, “Well, it’s a meritocracy, so you deserve what you get. Loser.”

From reading a lot of other academic blogs, and comments thereupon, I sense that a very particular path of success in research is presented to students that utterly buys into the meritocracy model and utterly discounts the lottery-like aspects of the career.

It could impede science more generally. People could be pursuing that last experiment, that last piece of data so that they can get it in a “better” journal, rather than publishing something that is perfectly interesting in its own right for others to see. People can get to be afraid of shipping.

For a supposed left-wing institution, academia often has some of the competitive elements associated with right-wing politics.

16 June 2010

“Helicopter parents” refers to adults who hover relentlessly around their kids at times when the kids should probably be trying to do things for themselves.

I propose there is a more advanced stage of this syndrome.

Armored car parentsn. Parents who attempt to transport their children from one secure point to another throughout life, abandoning any pretense of the offspring moving through life independently.

I arrive at this definition from this quote (from here), which disappoints me on so many levels.

(M)any evangelical parents seem to ask, “Is there someone in the virtual sphere where I can send my child where they can transition directly from a home-schooled environment into a collegiate environment and never leave the home?”

One of the undervalued aspects of schools, both grade schools and universities, is that they usually force you to meet people who are different than you. Who have different backgrounds, different ideas, different experiences, and who may (gasp!) actively disagree with you. For some people, school may be the only time in their lives they are actively challenged to articulate and justify their positions.

And some parents aren’t comfortable with that and want to take it away. Talk about living in a bubble.

Taking that experience away will leave those kids much duller and less prepared for that inescapable reality: There is more than one kind of person out there. And you’d better make some effort to get along with them.

15 June 2010

I saw this and could think of nothing but the alien from the movie Predator.

This is a frontal view of the head of a male Branchinecta brushi. This species of fairy shrimp is interesting in several ways. First, it is a species new to science, having just been described in a paper last week.

Second, this is one of the two highest crustacean species on the planet. There is one other crustacean found in the same pools that B. brushi is found in.

I also have to give this paper credit for the best opening line for a Materials and Methods section I may have ever read:

Dr. Charles F. Brush collected our specimens on 13 December 1988 during a successful bid to break the world record for high altitude SCUBA diving.

And yes, the species was named after the record holder who discovered and collected them.

The location of this successful world record bid was Cerro Paniri, a mountain in Chile. This image of the crater pond where this species was found gives a sense of what you have to do to break a world record in altitude, either for SCUBA or finding new species:

That’s 5,946 metres above sea level. This means crustaceans in these kinds of environments tend to have eggs that encyst, and can remain dormant for long periods until water returns, or be taken up and dispersed by birds. That this is particular species reproduces sexually also suggests that several cysts were introduced to the area by birds.

What’s slightly nerve wracking is that, as you can imagine, pools like this tend to come and go. This particular species is known only from the one collection in the one pool, and the authors suggest it might have evolved and speciated only in that pool. That makes it a good thing that it’s so high up, humans are unlikely to mess with it.

14 June 2010

If people were serious about their outrage about the Gulf oil spill, they wouldn't stop buying from BP, they'd try to stop buying gasoline.

Got a lot more attention and retweets and such than most things I put out (I think anything with BP is getting auto-tagged).

Note the use of the word, “try.” I know we’re in a fossil fuel economy and a lot of people can’t quit gasoline and still make a living. It would just be nice if people acknowledged that the demand for fossil fuels makes things like oil rigs possible, and that if it wasn’t BP out in the Gulf, it’d be someone else.

A little later, I found an article about boycotting BP that looks at the issue of boycotting BP.

My less than calm take on this is that listening to people hoping that BP goes bankrupt is like listening to addicts who want to find a better class of dope peddler.

The problem with writing about sea slug colouration is that they are so spectacular, so lovely, that you are tempted to turn the whole post into a photo gallery just to show off the pictures.

The bright colours are not there for just the benefit of lucky SCUBA divers. As I’ve noted before, sea slugs mollusks are perhaps the most appealing targets imaginable for a predator. When your entire body plan is essentially a predator’s “meals on wheels,” you might think the last thing you would want to do would be to draw attention to yourself.

Except that seas slugs are not as helpless as they might seem. They use chemicals extracted from the food they eat to make fairly nasty new chemicals. Predators do not like ingesting these chemicals, and some may well be toxic enough that if you ate one of these slugs, the predator might die.

Of course, making a predator sick after you’re in said predator’s digestive gland doesn’t do the slug any good, either. And that’s the problem with deterrents: they only work when everyone knows about them. (Corollary: If you ever develop a doomsday device, don’t keep it a secret.)

The theory that these bright colours are honest signals is more often intuited that tested. Just because SCUBA divers find sea slugs easy to see doesn’t mean that other animals do. Every animal has different sensory abilities, a different umwelt than humans. For instance, some fish see ultraviolet; many crustaceans are insensitive to red. And just because they seem very bright in an aquarium doesn’t mean they’ll stand out in the wild, where shades of the rainbow drop out the deeper you go.

You also have to reckon that at some point, there is going to be a point of diminishing returns. Even if you have a deterrent, there’s a point where you will draw so much attention to yourself that predators will attack either because they’re naive or starving or in error. (Corollary: Don’t go around being an ass even if you know kung fu, because sooner or later someone will wail on you anyway for being a jerk.)

Cortesi and Cheney keep quite a few of these balls in their air in this paper to figure out if, in fact, sea slugs’s bright colours are warning signs as predicted. They collected twenty sea slug species from their natural habitats, and took high quality images, including the ultraviolet, of both the slug and the environment it was found in.

To test whether this combination of colours of the slug on the background were conspicuous to fish, they used models of the kinds of colours that a couple of different fish species can see. The triggerfish (here) sees in the blue-green range; another species tested sees up into the ultraviolet. The authors admit that these species were chosen because we know about their visual systems, not because we know for certain that they eat all twenty of these sea slug species. Somewhere down the road, it would be nice if someone did behavioural tests with known sea slug predators.

The theory is that the most conspicuous sea slugs should be the ones that are the most toxic. To test toxicity, the authors ground up slugs, and put the extract in with brine shrimp eggs. Brine shrimp are pretty tough little creatures, but development is fairly fussy, and shrimp will be killed off by sea slug chemicals.

One of the most toxic is Sagaminopteron ornatum, shown here. Hypselodoris obscura, below that, is near the bottom of the toxicity list; the very bottom one I couldn't find a picture of searching the photo database as I usually do. I guess it’s just that plain-looking that nobody can be bothered to take a picture of it.

There is a correlation between conspicuousness and toxicity, regardless of what fish visual system they used to model this. There is a lot of variation, though, with the correlation explaining only about 7-12% of the variance.

The authors talk about several explanations to the rest of the variance. They talk about sexual selection, developmental variation, and the necessary simplification of the rampantly wild colour patterns into a more tractable measure of contrast. They also point out that while they measured toxicity, toxicity may not be as relevant a measure as palatability. There are plenty of foods that wouldn’t kill me or even make me sick, but I sure wouldn’t choose to eat voluntarily.

One of the other factors that they don’t raise is that there may be mimicry going on. Typically mimicry is considered to be between a pair of, or small number of species. But maybe there’s an element of bluffing that could be effective.

The authors also don’t discuss the possibility of individual variation. The methods are a bit vague on just how many individuals they used to test the toxicity. Considering that the chemical defenses are diet based, it’s entirely possible that toxicity fluctuates not only between individuals, but within an individual over time, as well.

Additional: Forgotten I’d bookmarked this lovely gallery from National Geographic. Like I said, you can’t help but end up making a slideshow.

The only proper response when an amateur attempts to hand you his manuscript... is to take an axe to his laptop, follow him home, burn down his house, and salt the ground.

But even more fun is Harlan Ellison reading a poem about why he will not read your fucking script. (In fact, this post is an elaborate contrivance to link to Ellison reading this poem.)

Scientists get far fewer amateurs asking them read things; I suppose that occasionally mathematicians have to put up with people claiming to be able to trisect an angle (i.e., cranks). But scientists are not only asked to read their colleagues’ work (sometimes by strangers), but they tend not to pull out the torches and pitchforks when they are asked. I'm not just talking about peer review; I'm talking about pre-submission work. I think the difference is that scientists are not paid directly for their writing, but only indirectly through "prestige," which may later generate grants and such.

10 June 2010

I was imitating Jean Chrétien a while ago to tell an anecdote to one of my students.

I could have done the greatest, most perfect, most spot-on, hysterical impersonation of Chrétien ever.* It all would have been lost on this student. An American undergraduate would be unlikely to recognize a Canadian prime minister, no matter how distinctive his speaking style was. (And it was. Oh, how it was.)

That’s the problem with imitation: it only works if both parties recognize what’s being imitated.

There’s imitation in the natural world, too, although it’s better known as mimicry. Almost everyone knows the example of the viceroy butterfly: tastes fine, but looks like the monarch butterfly, which tastes awful, so birds leave both alone because they can’t tell them apart. Thus, the viceroy gains an advantage. This is Batesian mimicry, named after Henry Bates. (Sean Carroll has a great bio of Bates in his book Into the Jungle.)

What if the viceroy butterfly and the monarch butterfly never met? Imagine that there was no overlap in their distributions at all? Now that would be a puzzle.

Those two butterflies do overlap, but a new review paper by Pfennig and Mullen argues that there are many cases where a mimic species occurs where the species its imitating does not. There are no cases where the mimic is completely isolated from the species it is mimicking, but the range of the mimic is often much greater than those of of the species being mimicked.

Pfennig and Mullen give examples of mimicking snakes that occur hundreds of kilometers away from the range of the model species. For the most part, there are only able to give crude estimates of how often the mimic is found without the model: basically, at this point, we’re unable to say little more than, “It happens.”

The paper lists several ways that we might be able to explain these distributions.

The first possibility is that mimicry really isn’t Batesian mimicry. For example, a species thought to be harmless might turn out not to be harmless (Müllerian mimicry). Alternately, both species have hit upon some sort of signal independently that predators avoid (convergent evolution).

Second, distributions of species are very dynamic. Just because the two species don’t overlap in some location now doesn’t mean that they have never done so. I like this idea, because it reminds us that things have a history.

Third, they discuss the possibility of hybridization leading to expansion for genes related to mimicry into new populations. Hybridization seems to occur quite a bit in butterflies, which are important models for mimcry, but this may not happen much in other species.

Fourth, the authors note that if a mimic is rare in arts of its ranges away from the model, it may not incur much of a cost, because many predators avoid feeding on unfamiliar foods. If anything, this paper underestimate the role that the predators could play in establishing the mimicking situation. If a long-lived, fairly smart predator feeds on the distasteful model at site A, it may remember that even if it encounters the mimic at site B very much later.

This review paper is a nice example of a review that tries to push the state of the art forward, and not just summarize.

09 June 2010

Our university had a 5% budget cut, an now is facing a 10% budget cut on top of that. Our situation is the new normal, according to a news piece in Nature that looks at the effects the financial crisis is having on universities. Also worth reading is an article on the financial benefits of investing in research (harder to prove than you might think).

One section, though, bugs me.

Diane Auer Jones... thinks budget pain should make smaller state schools rethink their research ambitions... (A)dministrators have been spending too much on programmes besides undergraduate education. Faculty members are rewarded on the basis of their research portfolios, and teaching gets mere lip service.

Not surprisingly, I disagree strongly with Jones (who also has an opinion piece in the issue).

First, if undergrad institutions are putting “too much” emphasis on research at the expense of teaching, what does that say about the heavily research intensive universities? They have far more notorious reputations for ignoring everything but research on tenure decisions.

Second, this advice reeks of something that “have” research universities would say. They would probably love to have less competition for money and resources.

I don’t believe for an instant that telling faculty that they should abandon their research and balkanizing undergraduate universities the way forward.

It’s one of the many deep flaws in my character. This may seem strange for someone who actively puts his title in the name of his main website and uses it as part of his Twitter name, but I realize that many people like formalities much more than I do. Robert Heinlein, so often good for a quote, wrote:

Moving parts in rubbing contact require lubrication to avoid excessive wear. Honorifics and formal politeness provide lubrication where people rub together. Often the very young, the untraveled, the naive, the unsophisticated deplore these formalities as “empty,” “meaningless,” or “dishonest,” and scorn to use them. No matter how “pure” their motives, they thereby throw sand into machinery that does not work too well at best.

A little note on academic formalities, then, for students, particularly those applying to a program or a grad school.

If you don’t know if a person should be addressed as “Doctor” or not, you haven’t done your homework.

It used to be easy to claim ignorance of someone’s academic credentials, but now, it’s hard to do so. You can usually uncover people’s academic credentials with a little Google stalking, particularly for people running programs.

Not everyone insists on being addressed by their title. I don’t (see above). But still, correct use of titles can be a signpost for several things.

One of my colleagues, who had a doctorate, told me that students – almost invariably male students – would refer to her as “Miss” or “Ma’am,” but would then turn around and refer to a male instructor as, “Doctor.” Even after this was pointed out to them. These were cases of macho bullshit, as far as we could tell.

And another thing, students: Never use “Dear Sir or Madame” in your email to your potential supervisor. If you can’t even figure out whether I’m a man or a woman, I sure as hell don’t want you in my lab.

As a gleeful thrower of sand, I never insist on formality. As a scientist, though, I almost always insist on accuracy.

Photo by russelljsmith on Flickr, used under a Creative Commons license.

08 June 2010

Beautiful little designs, radiating outward. A closer inspection reveals them to be tiny balls of compressed sand, with a small hole at the center.

This is something I have never had the good fortune of seeing on the beaches I’ve worked on. But now, if I was lucky enough to find this, I’d hazard a guess that it was the work on one of several species of crabs called sand bubbler crabs.

This sand bubbler crab was identified by the photographer as Dotilla fenestrata.

Beach picture by Edi Weissmann on Flickr; bubbles picture by Stewf on Flickr; Dotilla picture by Moon Fish on Flickr; all are used under a Creative Commons license.

For instance, in one of our recent papers, we pointed out that a reference given in another paper did not support the point being made (as far as we could tell). Probably most practicing scientists have a story like that. But how common is that sort of error?

A new paper by Todd and company claims that the error rate for peer-reviewed scientific journals in marine biology is about one in four.

That’s a bit of a surprise.

To come up with this number, they looked at one reference given in support of a claim from three articles of two issues of 33 journals (198 references total – pity they couldn’t have found a way to squeeze in two more to make it an even number). The authors say the reference was selected at random, but they didn’t really, because they only picked assertions that were supported by one reference, so a bit of selection is going on.

Although the title of the article claims one quarter of citations is “inappropriate,” the picture is not as bleak as the title suggests. In fact, only 6% of references did not support the claim being made; a figure closer to one in twenty than one in four.

The “one in four” comes from their claim that 75% of reference support the claim in the paper making them. The remaining 25% that they deem “inappropriate,” however, fall into several categories, and not all of those categories are equally problematic.

About 10% of citations are ambiguous, although the Todd and colleagues say they tended to give benefit of the doubt to those doing the citing. Annoying, but perhaps not damaging to the scientific literature.

The remainder of citations (7.6%) they deem “inappropriate” are cases where the claim is not supported by original data in the paper being cited, but in another paper that the cited paper itself cites. These are almost certainly people citing review articles. Todd and company argue that this is “inappropriate,” but this is surely debatable. Off the top of my head, here are some positive reasons to cite reviews:

Review articles often more cohesive than original articles

Easier to read text with a single citation than a long list of citations

Saves space

Can save time and effort for readers to track down only one article instead of a long series

Todd and company did look at impact factor of the journal the original paper doing the citing appeared in, with the unstated hypothesis being that “good” journals (i.e., higher impact factors) would have fewer inappropriate citations than “bad” journals. No relationship, which I think goes to show reviewers, and the review process, is a pretty homogeneous lot. (Every journal has a reviewer 2 who hates the paper.)

When initial discussion of this broke out on Twitter, Carin Bondar’s initial response was, “Impact factor is screwed!” I don’t think so. Impact factor would screwed only if there was some sort of systematic bias in which journals are being inappropriately cited. As far as I can tell, everything in this paper seems to suggest the errors are occurring at random. (Impact factors can be abused, but they provide a rough measure for authors to figure out if a journal has any credibility, which is a major problem in this day of experimentation in scientific publishing.)

Journal editors and reviewers should be the gatekeepers here. Reviewers should have some understanding of the relevant literature for the paper they are reviewing. But there are too few people to review too many papers, and it may be unreasonable for reviewers to do more than just a spot check. Maybe journals, particularly those of published by some of the extremely profitable academic publishers, could hire professional fact checkers. That a journal that had full-time fact checkers could easily be a selling point as a good impact factor.

That this article shows how easy it is to go and fact check these things shows, more than anything else, that the citation system works. We just don’t take enough advantage of the opportunities.